Prodigy
by KyraReid
Summary: They had met as kids, having saved her when she fell trying to reach her cat. Repeatedly. She had become a part of their little family. But then she left, leaving the brothers in the dark. Ten years later and now she's back. But they no longer know this woman, or if she can even be trusted. Until they find out what had happened to her after she left, and what she had done for them.
1. Chapter 1

_Dear Ms. Emmila L. Stones_

_After reviewing your work with Dr. Verarni within the lab as well as your solo accomplishments, it has been decided that your proposal will be accepted. We look forward to your future accomplishments._

_Congradulations Dr. Stones._

_Sincerely yours,_

_ Sylvia M. Burwell, 22__nd__ United States Secretary of Health and Human Services _

_ Regina M. Benjamin, 18__th__ Surgeon General of the United States_

Emmila read over the letter once again, a small smile crossing her face in victory. Ten years of hard work was finally beginning to come together. Now she was finishing up the last steps of this stage in her plans.

She was currently en route to New York City on a government owned jet, where she would be staying in an apartment until the preparations were finished. It was estimated to be a month or two until the center was ready. This gave her the perfect amount of time to fine tune a few details before the arrival of her team.

Emmila looked over the file in her hands. It had been dangerous work obtaining it, earning her more than a few new enemies. Undoubtedly her friends would be furious if they found out what she had done to get it. But that was if they remembered her. Halfway through her Bachelor's degree she had been forced to stop nearly all contact with them, only managing to sneak a few emails throughout the years. But even that had stopped three years ago.

She traced over the front picture of the file, feeling nostalgic. Everything she had done the past ten years was for one goal, and that was to protect her dear friends. But once she set all of her cards on the table, Emmila could not help but wonder if they would want anything to do with her. She would not blame them. Doctors and scientists like her were hardly the best people in the world. Their own run-ins with people like her had rarely been in their favor.

Emmila turned her attention to the small television. The channel was showing an interview from a few days ago. The Surgeon General was speaking to the cameras about the new facility being built just outside the city. Beside her was Emmila, and behind Emmila was a small group of people who would make up her team. The older woman gestured for Emmila to take over the interview.

* * *

Four brothers watched the television with mixed emotions as they watched the interview.

"_My name is Doctor Emmila Stones, and the leader of this program. It is our hope and belief that with the creation of this facility and this team of experts that we will be able to create a cure for genetic diseases and replicate our findings throughout the world."_

"Hey, that's really her, right?" The normally happy joker was quiet as he asked his question.

"It's definitely her alright." There was no mistaking their old friend, no matter how many years had gone by, the genius of the group had done his best to keep tabs on her.

"She really coming home? Not a word from her in how many years, and all of a sudden, she comes home without a by your leave?!" The hot headed brother ranted, his voice cracking with pain despite his apparent anger. But it was their eldest brother who was affected the most.

"Be careful. Time can change people. With what she's gotten into, who knows what her motive for coming back is."

"But this is Emmila. There's no way she's bad. Right?" None of his elder brothers could answer the question.


	2. Chapter 2

Emmila cursed under her breath to high heaven and back as she followed her cat through the ally it had taken off in. She finally found the white feline perched on an overhang above her head. A pile of crates next to it explained how it had happened.

"Damn cat. I knew I should have left you back there. Not even a few hours and you're already causing me problems."

The cat blinked at her with its mismatched eyes before meowing.

"Don't you meow me you ungrateful brat. Stay there while I get you." Gingerly, Emmila began to climb the crates to get to her cat.

She was several feet off the ground when an ominous crack sounded out. The crate beneath the one Emmila was standing on had caved in. She barely had time to gasp out in surprise as her crate went tumbling down, taking the young woman with it.

It was only when her brain registered that her body had not impacted the ground that her eyes shot open. Green met blue as she looked into a very familiar face. One that she had not seen in person in many years.

"Leo…" His name came out as a whisper from the shocked woman. The mutated turtle carefully set her down, having caught her during her fall, and took a step back from the woman.

"I'm certain that we told you to not climb things in an ally before." He chided her. To hear his voice again brought back so many memories. It was deeper than before, but still the same. To cover up her trip in memory lane, she jabbed her finger in the direction of her cat.

"Tell that damn cat to stop going where she shouldn't then."

"I got her dudette." Another figure jumped to the ledge where her cat was. Emmila recognized Mikey as he scooped up her cat and landed next to her. The cat leapt from his arms and landed on Emmila's shoulder, a move so familiar that it had the orange clad turtle grinning.

Near silent thumps were heard as Raph and Donnie joined the group. Before Emmila had left, events like this had been common place. It had been the reason Emmila met the brothers, and after the first few times of watching her chase down the cat and getting into trouble, they had begun to go with her. But a lot had changed since then.

Emmila could feel the intense gazes of the brothers as they observed her, and likewise she took a good look at them. They had gained many battle scars over the past decade and grown in height and muscle. There was an air of wariness and tension about them that had not been there before. The four of them easily reached past six foot, though Mikey was still shorter that his brothers. It was Donnie who was the tallest, though he was more slender than his brothers. Raph was built like a tank, out muscling all of his brothers. But Leo was exactly how she pictured him to be as he stood proudly. It made her quirk a smile.

Just as they had changed, Emmila had changed as well, and the four of them took the changes in as they looked at her. Gone was the fourteen year old girl they knew. The Emmila before them was a twenty-four year old woman. Her brown hair was pulled up in a messy bun, and even though they could still see the warmth in her eyes, the hard and worn look on her face overshadowed it. It made Leo wonder what she had gone through in her absence.

"When did you get back?" Leo's voice was wary and Emmila had to fight down a frown. She had known they would not trust her after all.

"Only a few hours ago."

"Why'd you come back, after so long?" Emmila's green eyes met Leo's own blue ones, the look in her eyes very serious. It put the four turtles on edge.

"It's a long story, one you won't like too much most likely."

"We've got time." She had known he would say that.

"Very well. But not here." Before they could protest, Emmila cut them off with a bitter grin.

"I do have enemies. Many of them would love to have me shot in an ally." The brothers frowned. What had their friend been doing?

* * *

Emmila ushered them into her apartment before locking all the doors and windows and pulling the curtains closed. As she ran about, the brothers took in the place. Obviously she had not finished unpacking. Boxes were stacked in corners, overflowing with papers and binders. The dining room table was the only thing not covered with papers and it was there that Emmila sat, several folders in front of her. The four brothers took seats across from her.

Emmila slid one of the files towards them and Leo opened it. It was a file on Emmila and her research.

"As you know, I went into genetic research. But it was mutations that I specialized in." They looked up at her sharply before returning to the file. Another one was slid towards them.

"I worked with a lot of high ranking scientists and doctors. Some I'm ashamed to admit the names of." The file was about them. The amount of information in it made their blood ran cold.

"Where did you get all of this?" Leo was shaking, though his voice remained level.

"I won't tell you the details. But those files are why I made enemies." The rest of the files slid towards them. Some were far thinner than the second one; many of them contained the same information though.

"Those files are part of the reason why I came back. I figured you would want them." She steepled her fingers in front of her.

"Emmila, how did you get this?" Leo's tone was sharp. Emmila gave a smile that matched his tone.

"I stole them obviously."


	3. Chapter 3

Leonardo's felt a pit in his stomach grow at her words. Whoever had this much information on him and his brothers was undoubtedly very powerful and very dangerous. But it was Donatello that spoke first.

"You stole confidential documents?" He asked in disbelief.

Emmila leveled a look at him. "They were not supposed to have this information. And some of them should never have it. There's a lot in there about you guys. Particularly in the first two files.

The brothers went back over the first two files again, the pit in the eldest brother's stomach continuing to grow. Things in those files were very familiar. The implication filled them with dread.

"Who did you take these from?" Leonardo asked quietly.

Emmila hesitated. Despite being gone for ten years, the woman had in fact kept close tabs on the brothers. She knew how they would react to the names of the men she took the files from. It would not be pleasant. But they were getting impatient.

"Emmila!" Raphael snapped at her, causing the woman to close her eyes and sigh.

"Bishop and Stockman." Chaos erupted in around her as the four mutated brothers leapt to their feet, knocking over their chairs, shouting. But it was Michelangelo who surprised her.

The youngest brother and her always had a close sibling bond, and as a result, Michelangelo was fiercely protective of what he considered his little sister.

"What were you thinking Em! Do you have any idea how dangerous they are?" The fear in his eyes was for her safety. Ten years and that had not changed. Emmila kept her face unaffected.

"They will kill you Em!" Donatello was right there with his little brother. "Bishop is insane! He'll stop at nothing to remove a threat, and Stockman is a power hungry evil scientist! Now you've gone and marked yourself as a threat to both of them!"

"And now ya came back to the city, a place more dangerous for you than anywhere else!" Raphael growled at her.

But it was Leonardo, who's voice was the quietest, that cut the deepest.

"Why did you come back?"

Emmila opened her eyes, having closed them during the ranting, and ignored the anger in his own blue ones. The woman stood from her seat and began going through some of her boxes, organizing them and putting things away.

"In a month the facility will be ready for living. My team and I will be staying there once they arrive. It is safer there than anywhere else." She cut a look at Michelangelo, who opened his mouth to say something, and shut him down. "Including the Lair."

Emmila turned back to what she was working on. "You have been sent to other worlds and alternate dimensions while in the Lair. Master Splinter was turned into data bits, of all things, before Donatello was able to bring him back. Not to mention those damnable mousers destroyed the first one, causing you to relocate. Even the Foot has invaded it before."

Leonardo felt cold. How did Emmila know all of this? But the woman was continuing her rant, preventing him from asking.

"Why did I return? Is it truly that hard to believe I missed you lot? I told you that my work prevented me from contacting you! So I took the first chance I've had in years, and came back. I'm a doctor first and a scientist second. Not some damn heartless monster. Cold? Yes. But never a monster."

The brother watched her warily as Emmila began to stack boxes of papers in a corner. The woman was panting from either the exertion or her ranting, they were unsure.

"In the time that I have been gone from your sight I have been working my ass off, making a name for myself. I'm known enough that, as long as I'm around, Bishop can't go directly after you. I'm in his way and if he removes me, too many questions would be raise and trouble he does not want would land on him."

Emmila was on a role, moving boxes and spewing out words unfalteringly.

"Stockman, that pathetic excuse for a scientist, hates me with a surprising amount of fury. But he is unable to get his own hands on me due to the defense I have created against him." Emmila continued to work, refusing to look at the brothers. The next time that she spoke it was much quieter.

"For ten years I have been gone. I have seen things I wish I never had and will never be able to forget, no matter how much I wish I could. You see me as a potential threat."

Michelangelo and Donatello voiced their objections at that last bit but Emmila cut them off.

"Do not deny it. I can see it in the way your hold yourselves and in the air around you. But it is something I can fully understand. You know me to be a scientist, one who specializes in mutations. The mutagen in your blood makes you a treasure trove for people in my profession. Your belief that I have abandoned you only reinforces it. You are free to believe what you want, I will not argue against it. But don't you dare underestimate me."

Emmila's eyes flashed with a strong, but unreadable, look. It froze the four brothers to their spots.

"Regardless of what you think, I have kept constant tabs on you all. I know about Leatherhead, the Kraang, the Foot and Shreader. I know about your trips to other worlds and dimensions and the year you were sent to the future. I know of April O'Neil and Casey Jones. I even know about Klunk."

Emmila finally gave a brief look to the turtles, but they could not discern the look on her face before she turned back to her work.

"I know, Leonardo, that you left the country to South America for almost two years. I know, Raphael, that you were the Nightwatcher. I know Donatello took on a tech job and Michelangelo worked at children's parties."

Emmila's eyes returned to her work. "I know how many times you have saved the world, and even multiple worlds. Just as I know how many times you almost died. I have personally run into Bishop and Stockman. You may think what you like, but I did not abandon you."

So engrossed in what she was doing, Emmila did not see the box behind her. The woman took a step back and fell backwards. For the second time that night, Emmila found her green eyes looking into Leonardo's blue ones.

"Did they hurt you?" His voice was soft, but Emmila could hear the promise behind it. He would personally hunt down the ones who caused her pain.

For a moment Emmila was unable to breath, the familiarity of his actions slamming into her. Leonardo saw something brief flash across her face before it was gone, but he had seen it, no matter how fast she had tried to hide it. Emmila straightened up and took a step away.

"Going after them would defeat the purpose of me being here. I am alive and well now, Leonardo." The blue clad turtle frowned as Emmila continued to step away.

"Those files are yours. Destroy them if you want. I'm going to bed. Lock up on your way out."

The brothers watched as their old friend disappeared into a bedroom and shut the door. It was silent as they took their leave.

Emmila waited until she was certain they had left before sliding down to sit against her door. She had not been prepared to confront the turtles yet. This had sent things ahead by quite a bit. The woman stood up. She had to make a few calls.


	4. Chapter 4

The trip back to the Lair was silent, the four brothers caught in their own thoughts. It was not until they had entered their home that Mikey broke the silence.

"She's so cold." He was subdued. Raph but an arm around his baby brother to give him a little comfort.

"I don't think she's a threat though." Donnie told them.

"She ain't a helper either." Raph spat back. Donnie frowned at his temperamental brother.

"If she was going to do something, she would already have done it. Em knew when we were weak. In genetic engineering, mutants like us are gold mines, but not once did she come after us."

"She didn't make sure we were ok either. Em ain't the Em we knew!" So upset by the situation, Raph took no notice of his use of Emmila's nickname.

"Don." Leo broke into their argument, causing them all to turn to him.

"If she was able to keep such a close watch on us, then there has to be a way to find out what Emmila's been up to these past ten years."

Donnie got what Leo was implying. He nodded. "On it."

The genius took off to his lab, leaving Raph to wander off to his own room, where he would most likely be blowing off steam.

Mikey took a seat on the couch in front of his older brother, petting Klunk who had jumped into his lap. Leo stood there, waiting for his baby brother to speak, knowing he would.

"I think something really bad happened to Em." Mikey had always been close to Em. The two had shared a sibling-like bond that had almost rivaled the brothers own.

"We will find them." Mikey looked up into Leo's eyes.

"Em's in a lot of danger, and I think it's because of us. Remember what she said before she left?"

Leo remembered, it was something none of them would ever forget. Mikey continued speaking.

"With her profession, she's bound to run into any mention of us and face people like Bishop and Stockman. But instead of using the information she has personally on us, Em has been risking her life to hide and steal the information people have found about us. She has been protecting us for who knows how long. And it had gained her a lot of enemies, ones we probably have no idea about."

Leo really hated how logical Mikey could be when he was serious.

* * *

It was three days later when Donnie's shout had his three brothers running to the lab.

"Find anything?" Mikey was the first one to ask. A frown marred Donnie's face.

"I almost had something but someone blocked me." There was a stunned silence.

"Bro, you're one of the smartest people around. No one can block you." Raph told him in disbelief. The other two were in agreement. There was no way Donnie had been blocked.

"Well it just happened." Donnie snapped as he tried to fight back against this new barrier.

"The hell is going on?" His fingers flew over the keyboard as he tried to keep up with the threat. Every angle, every corner an every hole, no matter how small, was being blocked.

* * *

"So this is them? Pretty persistent if you ask me." The redhead female commented as she watched over the shoulder of her coworker.

"Yeah. I don't know how long I can keep him out." The blond sitting at the keyboard replied, hands flying over the keys.

"If you can't keep him out, then shut him down." The girls looked over to their boss.

"Oh? I thought you wanted to play nice." The redhead leaned back, stretching as she commented her thoughts. Their leader shook her head.

"No time for that now." Turning to the remaining blond, she began to give instructions. "Make sure the security is all set up. We'll be moving in sooner than expected."

"Got it." Their boss left, pulling out a phone. They really needed to stop looking for things they should not be.

* * *

Mikey, Leo and Raph were watching Donnie intently when Mikey's shell-cell rang. He looked in confusion at the unknown number before answering it.

"Hello?"

"_You have ten seconds before the computer gets fried." _All the brothers heard the voice that came over the speakers. Donnie began to curse as he quickly backed out of everything and shut down his system.

"Em? What are you doing?" Mikey questioned the girl in confusion and worry.

"A better question would be, what are you hiding from us, Em." Leo's hard voice was heard by the girl on the other side of the line. She gave a weary sigh.

"_It's better you don't know. Please stop looking."_ With a click she hung up, leaving the brothers in silence.

"What the hell!" Raph stormed out of the lab, heading to his room to vent his anger. Leo watched him go before turning back to Donnie.

"Were you able to find anything on her?"

"Nothing real useful. Just whatever was in the press and a few hospital records."

"Hospital records?" Leo and Mikey shared a glance. Donnie nodded and held out some papers he had printed earlier, his face grim.

"Looks like she was assaulted a few times. Broken bones, internal bleeding and a few lacerations and burns. She was admitted to the hospital at least four or five times, maybe more." Leo felt a pit grow in his stomach as Donnie fixed them with a hard look.

"After Em left, for the first few months she kept in constant contact with us before sending a message once or twice a month until six years ago. Leo, these attacks started around the same time we lost all contact with her."

Mikey felt tears well up in his eyes as Leo clenched his fists together. There was only one reason for that to have happened to her.

"She was protecting us." Raph leaned against the door frame, eyes dark. Donnie nodded.

"Yeah, this whole time."


End file.
